Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 4 | 16.88 |
PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).
Antibiotic resistance genes
Comprehensive Antibiotic Resistance Database (CARD)
| Query ID | Begin | End | ARO name | ARO accession | CARD name | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| NMMECHGA_1 | 2771715 | 2772569 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| NMMECHGA_1 | 2742191 | 2743393 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| NMMECHGA_1 | 2548132 | 2549301 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NMMECHGA_1 | 1397952 | 1398269 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NMMECHGA_1 | 1397614 | 1397952 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NMMECHGA_1 | 936842 | 939412 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| NMMECHGA_1 | 650255 | 651898 | vmlR | ARO:3004476 | vmlR | 98.90 | 100.00 | NC_000964.3 |
| NMMECHGA_1 | 387687 | 388280 | tmrB | ARO:3003059 | tmrB | 98.98 | 100.00 | AL009126.3 |
| NMMECHGA_1 | 337206 | 338639 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.00 | JYFL01000006.1 |
| NMMECHGA_1 | 324858 | 325778 | mphK | ARO:3004541 | mphK | 97.39 | 100.00 | CP010314.1 |
RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)
ResFinder
| Query ID | Begin | End | Resistance gene | Phenotype | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|
| NMMECHGA_1 | 4306952 | 4308328 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.84 | 100.00 | D12567 |
| NMMECHGA_1 | 2771715 | 2772569 | aadK | Streptomycin | 98.60 | 100.00 | M26879 |
| NMMECHGA_1 | 324858 | 325778 | mph(K) | Spiramycin, Telithromycin | 96.96 | 100.00 | NC_000964 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| NMMECHGA_1 | 4306955 | 4308328 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| NMMECHGA_1 | 650258 | 651898 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.90 | 100.00 | WP_003234144.1 |
| NMMECHGA_1 | 2771718 | 2772569 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| NMMECHGA_1 | 324858 | 325775 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.39 | 100.00 | WP_003246254.1 |
| NMMECHGA_1 | 4304431 | 4304949 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| NMMECHGA_1 | 2111491 | 2114088 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.29 | 100.00 | WP_087347987.1 |
AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)
Virulence factors
Virulence Factor Database (VFDB)
| Query ID | qstart | qend | Gene name | e-value | VF name | VF category | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|---|
| NMMECHGA_1 | 3814537 | 3815718 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NMMECHGA_1 | 3402749 | 3403687 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| NMMECHGA_1 | 2345314 | 2345955 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| NMMECHGA_1 | 3405363 | 3406559 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.42 | 100.00 | NP_391079 |
| NMMECHGA_1 | 3812912 | 3814054 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| NMMECHGA_1 | 3406585 | 3407370 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.24 | 100.00 | NP_391080 |
| NMMECHGA_1 | 3814073 | 3814522 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| NMMECHGA_1 | 2065699 | 2067462 | dep/capD | 0.0 | Capsule | Immune modulation | 99.09 | 100.00 | NP_389723 |
| NMMECHGA_1 | 3395593 | 3402729 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.92 | 100.00 | NP_391076 |
| NMMECHGA_1 | 3403715 | 3405334 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.64 | 100.00 | NP_391078 |
BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)
VirulenceFinder
| Query ID | Begin | End | Database | Virulence factor | Protein function | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)
Pathogenic genes
PHI-base
| Query ID | qstart | qend | Gene name | e-value | Function | Identity | Coverage | Gene ID |
|---|---|---|---|---|---|---|---|---|
| NMMECHGA_1 | 132340 | 133476 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| NMMECHGA_1 | 18602 | 19471 | pdxS | 3.22e-149 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NMMECHGA_1 | 1708719 | 1709495 | CodY | 3.52e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NMMECHGA_1 | 3657846 | 3658415 | ClpP | 2.61e-98 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| NMMECHGA_2 | 4935 | 5121 | Col(SD853) | 187 / 194 | 88.24 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NMMECHGA_1 | 0.0 | 1.0 | 0.0 |
| NMMECHGA_2 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NMMECHGA_1 | 168176 | 174502 | False | Unknown | VOG9667, VOG9667, VOG8241, VOG3549, VOG1878, VOG0083, VOG1309 |
| NMMECHGA_1 | 186768 | 211957 | False | Myoviridae | VOG9315, VOG4773, VOG4688, VOG4685, VOG0749, VOG1581, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG0906, VOG7718, VOG3390, VOG7895 |
| NMMECHGA_1 | 1340169 | 1367750 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| NMMECHGA_1 | 1912666 | 1934461 | False | Siphoviridae | VOG4841, VOG4581, VOG4544, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG3390, VOG4705, VOG4612, VOG3390, VOG4705 |
| NMMECHGA_1 | 2297701 | 2314862 | False | Siphoviridae | VOG4662, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG7900 |
| NMMECHGA_1 | 3234921 | 3256278 | False | Siphoviridae | VOG4574, VOG0136, VOG0753, VOG5535, VOG4599, VOG4605, VOG9745, VOG0701, VOG10044, VOG0698, VOG0697, VOG0696, VOG0695, VOG2621, VOG4572, VOG9317, VOG0692, VOG0691, VOG10227, VOG0796, VOG7983, VOG0198 |
| NMMECHGA_1 | 3280339 | 3296792 | False | Siphoviridae | VOG5042, VOG4910, VOG4713, VOG4553, VOG4555, VOG0720, VOG5023, VOG0221 |
Phigaro v2.4.0 (Database: Jan. 2024 release)